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- PDB-5jx3: Wild type D4 in orthorhombic space group -

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Basic information

Entry
Database: PDB / ID: 5jx3
TitleWild type D4 in orthorhombic space group
ComponentsUracil-DNA glycosylase
KeywordsHYDROLASE / DNA Repair Enzyme Component of Processivity Factor Poxvirus
Function / homology
Function and homology information


uracil-DNA glycosylase / uracil DNA N-glycosylase activity / DNA repair / DNA binding
Similarity search - Function
Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uracil-DNA glycosylase
Similarity search - Component
Biological speciesVaccinia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSchormann, N. / Chattopadhyay, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5U01-AI-082211 United States
CitationJournal: Protein Sci. / Year: 2016
Title: Poxvirus uracil-DNA glycosylase-An unusual member of the family I uracil-DNA glycosylases.
Authors: Schormann, N. / Zhukovskaya, N. / Bedwell, G. / Nuth, M. / Gillilan, R. / Prevelige, P.E. / Ricciardi, R.P. / Banerjee, S. / Chattopadhyay, D.
History
DepositionMay 12, 2016Deposition site: RCSB / Processing site: RCSB
SupersessionJun 29, 2016ID: 2OWR
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2017Group: Database references
Revision 1.2Aug 9, 2017Group: Database references / Category: pdbx_related_exp_data_set / Item: _pdbx_related_exp_data_set.data_reference
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.4Aug 15, 2018Group: Data collection / Database references / Category: pdbx_related_exp_data_set / Item: _pdbx_related_exp_data_set.data_reference
Revision 1.5Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.7Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uracil-DNA glycosylase
B: Uracil-DNA glycosylase
C: Uracil-DNA glycosylase
D: Uracil-DNA glycosylase
E: Uracil-DNA glycosylase
F: Uracil-DNA glycosylase
G: Uracil-DNA glycosylase
H: Uracil-DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,43527
Polymers202,9128
Non-polymers1,52319
Water14,412800
1
A: Uracil-DNA glycosylase
B: Uracil-DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1897
Polymers50,7282
Non-polymers4605
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Uracil-DNA glycosylase
D: Uracil-DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1327
Polymers50,7282
Non-polymers4045
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Uracil-DNA glycosylase
F: Uracil-DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1327
Polymers50,7282
Non-polymers4045
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Uracil-DNA glycosylase
H: Uracil-DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9836
Polymers50,7282
Non-polymers2554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.769, 134.065, 139.101
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Uracil-DNA glycosylase / UDG


Mass: 25364.029 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus (strain Western Reserve)
Strain: Western Reserve / Gene: UNG, TS17, VACWR109, D4R / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: P04303, uracil-DNA glycosylase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 800 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsWestern Reserve (WR109) vaccinia virus strain was used. The closest sequence database entry is: ...Western Reserve (WR109) vaccinia virus strain was used. The closest sequence database entry is: AA089388. Any sequence difference from this entry except for the engineered mutations in the D4 mutants is unintentional

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 55.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 5% PEG3000, 0.1M NaCl, 0.1M Hepes

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.9762 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 17, 2005 / Details: Mirrors
RadiationMonochromator: Double Crystal Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.3→32.24 Å / Num. obs: 98092 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 7.48 % / Biso Wilson estimate: 28.6 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.4
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7.48 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DOF_A

Resolution: 2.3→32.24 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.905 / SU B: 6.613 / SU ML: 0.163 / Data cutoff high absF: 0 / Cross valid method: THROUGHOUT / ESU R: 0.34 / ESU R Free: 0.234 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24853 4905 5 %RANDOM
Rwork0.2152 ---
obs0.21688 93226 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.778 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å2-0 Å2
2---0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.3→32.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14100 0 94 800 14994
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01914631
X-RAY DIFFRACTIONr_bond_other_d0.0020.0213902
X-RAY DIFFRACTIONr_angle_refined_deg1.2231.95119872
X-RAY DIFFRACTIONr_angle_other_deg0.942332102
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.12551747
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.26624.137643
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.106152482
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3141560
X-RAY DIFFRACTIONr_chiral_restr0.0710.22203
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02116128
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023352
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1383.3346994
X-RAY DIFFRACTIONr_mcbond_other1.1383.3346993
X-RAY DIFFRACTIONr_mcangle_it2.0164.9918739
X-RAY DIFFRACTIONr_mcangle_other2.0164.9928740
X-RAY DIFFRACTIONr_scbond_it0.983.4467637
X-RAY DIFFRACTIONr_scbond_other0.983.4467637
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7655.10411134
X-RAY DIFFRACTIONr_long_range_B_refined3.97126.35416908
X-RAY DIFFRACTIONr_long_range_B_other3.80526.26416586
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 369 -
Rwork0.262 6808 -
obs--99.9 %

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